Opened 3 years ago

Closed 3 years ago

#7507 closed defect (nonchimerax)

vop resample: glClear: invalid framebuffer operation

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/mizimmer/Dropbox/from_wustl_box/Documents/WUSTL_PostDoc_FremontLab/projects/alphaviruses/WEEV/WEEV_mxra8_chimera/cryosparc/3d_class/run_ct2_it012_class001.mrc
> /Users/mizimmer/Dropbox/from_wustl_box/Documents/WUSTL_PostDoc_FremontLab/projects/alphaviruses/WEEV/WEEV_mxra8_chimera/cryosparc/3d_class/run_ct2_it012_class002.mrc
> /Users/mizimmer/Dropbox/from_wustl_box/Documents/WUSTL_PostDoc_FremontLab/projects/alphaviruses/WEEV/WEEV_mxra8_chimera/cryosparc/3d_class/run_ct2_it012_class003.mrc
> /Users/mizimmer/Dropbox/from_wustl_box/Documents/WUSTL_PostDoc_FremontLab/projects/alphaviruses/WEEV/WEEV_mxra8_chimera/cryosparc/3d_class/run_ct2_it012_class004.mrc

Opened run_ct2_it012_class001.mrc as #1.1, grid size 280,280,280, pixel 1.2,
shown at level 2.25e-06, step 2, values float32  
Opened run_ct2_it012_class002.mrc as #1.2, grid size 280,280,280, pixel 1.2,
shown at level 8.4e-06, step 2, values float32  
Opened run_ct2_it012_class003.mrc as #1.3, grid size 280,280,280, pixel 1.2,
shown at level 3.34e-06, step 2, values float32  
Opened run_ct2_it012_class004.mrc as #1.4, grid size 280,280,280, pixel 1.2,
shown at level 3.84e-05, step 2, values float32  

> volume step 1

> hide #!1.4 models

> hide #!1.3 models

> hide #!1.2 models

> volume #1.1 level 0.0003395

> volume #1.1 level 0.002498

> show #!1.2 models

> hide #!1.1 models

> volume #1.2 level 0.001916

> volume #1.2 level 0.0007716

> show #!1.3 models

> hide #!1.2 models

> volume #1.3 level 0.002498

> volume #1.3 level 0.0006101

> show #!1.4 models

> hide #!1.3 models

> volume #1.4 level 0.001256

> show #!1.2 models

> hide #!1.2 models

> hide #!1.4 models

> show #!1.2 models

> show #!1.3 models

> hide #!1.2 models

> volume #1.3 level 0.0006775

> show #!1.4 models

> hide #!1.3 models

> show #!1.3 models

> show #!1.1 models

> hide #!1.3 models

> hide #!1.4 models

> volume #1.1 level 0.0027

> show #!1.2 models

> hide #!1.1 models

> volume #1.2 level 0.0006444

> show #!1.3 models

> hide #!1.2 models

> volume #1.3 level 0.0003404

> volume #1.3 level 0.001082

> volume #1.3 level 0.0027

> hide #!1.3 models

> show #!1.4 models

> volume #1.4 level 0.001324

> show #!1.2 models

> hide #!1.4 models

> volume #1.2 level 0.00427

> volume #1.2 level 0.001726

> show #!1.1 models

> hide #!1.2 models

> volume #1.1 level 0.003442

> show #!1.3 models

> hide #!1.1 models

> volume #1.3 level 0.0008798

> hide #!1.3 models

> show #!1.2 models

> hide #!1.2 models

> volume #1.2 level 0.00039

> volume #1.2 level 0.0007716

> volume #1.3 level 0.0006775

> hide #!1.2 models

> hide #!1.3 models

> show #!1.1 models

> volume #1.1 level 0.000272

> hide #!1.1 models

> show #!1.4 models

> volume #1.4 level 0.001324

> volume #1.4 level 0.001459

> show #!1.2 models

> show #!1.3 models

> hide #!1.4 models

> show #!1.4 models

> close #1

> close #

Expected a models specifier or a keyword  

> open
> /Users/mizimmer/Dropbox/from_wustl_box/Documents/WUSTL_PostDoc_FremontLab/projects/alphaviruses/WEEV/WEEV_mxra8_chimera/cryosparc/cryosparc_P15_J27_011_volume_map.mrc

Opened cryosparc_P15_J27_011_volume_map.mrc as #1, grid size 280,280,280,
pixel 1.2, shown at level 0.193, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.2492

> volume #1 level 0.2185

> volume #1 level 0.2925

> volume #1 level 0.2384

> volume #1 level 0.2654

> open
> /Users/mizimmer/Dropbox/from_wustl_box/Documents/WUSTL_PostDoc_FremontLab/projects/alphaviruses/WEEV/WEEV_duck_mxra8_2/model_building/RealSpaceRefine_25/RSR24_coot_touchup_real_space_refined_025.pdb

Chain information for RSR24_coot_touchup_real_space_refined_025.pdb #2  
---  
Chain | Description  
A B C L | No description available  
D F H J | No description available  
E G I K | No description available  
  

> ui mousemode right "rotate selected models"

> select #2

68968 atoms, 69952 bonds, 4484 residues, 1 model selected  

> view matrix models
> #2,0.73684,-0.13554,0.66235,-44.687,0.011196,0.98201,0.18849,-29.587,-0.67598,-0.13147,0.7251,172.42

> view matrix models
> #2,0.56687,0.35937,0.74129,-114.79,-0.021214,0.90591,-0.42295,88.497,-0.82353,0.22403,0.52116,168.73

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.56687,0.35937,0.74129,-106.16,-0.021214,0.90591,-0.42295,90.714,-0.82353,0.22403,0.52116,167.32

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.46664,-0.081615,-0.88067,249.69,0.41542,-0.85883,0.29971,202.51,-0.78081,-0.50571,-0.36686,429.46

> ui tool show "Fit in Map"

Fit molecule RSR24_coot_touchup_real_space_refined_025.pdb (#2) to map
cryosparc_P15_J27_011_volume_map.mrc (#1) using 68968 atoms  
average map value = 0.1309, steps = 168  
shifted from previous position = 18.5  
rotated from previous position = 14.4 degrees  
atoms outside contour = 56815, contour level = 0.26544  
  
Position of RSR24_coot_touchup_real_space_refined_025.pdb (#2) relative to
cryosparc_P15_J27_011_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.49835765 -0.31836072 -0.80640319 283.11263707  
0.29872703 -0.81012320 0.50444282 163.78484484  
-0.81388072 -0.49228737 -0.30862814 427.10498125  
Axis -0.85022330 0.00637842 0.52638356  
Axis point 0.00000000 165.77403837 269.98483356  
Rotation angle (degrees) 144.11516844  
Shift along axis -14.84323374  
  

> ~select #2

Nothing selected  

> molmap protein 15

Opened RSR24_coot_touchup_real_space_refined_025.pdb map 15 as #3, grid size
55,49,52, pixel 5, shown at level 0.0576, step 1, values float32  

> volume #3 level 0.01776

> volume #3 level 0.01

> volume #3 level 0.001139

> volume #3 level 0.001

> vop resample #3 onGrid #1

Opened RSR24_coot_touchup_real_space_refined_025.pdb map 15 resampled as #4,
grid size 280,280,280, pixel 1.2, shown at step 1, values float32  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 82, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 148, in status  
r.draw_background()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000033b18f0>
contents scale of 2 - updating layer to match.  




OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.9 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 451.120.7.0.0
      OS Loader Version: 540.120.3~6
      SMC Version (system): 2.45f5

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 3 days 2:38

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AU-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        LS32A600N:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: HCPR400069  
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    MolecularDynamicsViewer: 1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → vop resample: glClear: invalid framebuffer operation

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed

This appears to be a Qt bug on Mac related to dual displays, especially when one display is retina and one is not.

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000033b18f0> contents scale of 2 - updating layer to match.

Possibly ChimeraX was running on the laptop display and then they closed the laptop and it moved to the external display.

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